From c8805abb1d906a556fb97808959670a71a9bb491 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 5 Dec 2017 12:39:23 +0000
Subject: [PATCH] JAL-2847 added pfam to DBRef source name lookup

---
 src/jalview/util/DBRefUtils.java |   20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 50a34fc..203b4e7 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -43,9 +43,9 @@ public class DBRefUtils
   /*
    * lookup from lower-case form of a name to its canonical (standardised) form
    */
-  private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+  private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
 
-  private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
+  private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<>();
 
   static
   {
@@ -65,6 +65,8 @@ public class DBRefUtils
     canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
     canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
 
+    canonicalSourceNameLookup.put("pfam", DBRefSource.PFAM);
+
     // Make sure we have lowercase entries for all canonical string lookups
     Set<String> keys = canonicalSourceNameLookup.keySet();
     for (String k : keys)
@@ -97,13 +99,13 @@ public class DBRefUtils
     {
       return dbrefs;
     }
-    HashSet<String> srcs = new HashSet<String>();
+    HashSet<String> srcs = new HashSet<>();
     for (String src : sources)
     {
       srcs.add(src.toUpperCase());
     }
 
-    List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> res = new ArrayList<>();
     for (DBRefEntry dbr : dbrefs)
     {
       String source = getCanonicalName(dbr.getSource());
@@ -218,7 +220,7 @@ public class DBRefUtils
   static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
           DbRefComp comparator)
   {
-    List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> rfs = new ArrayList<>();
     if (refs == null || entry == null)
     {
       return rfs;
@@ -594,7 +596,7 @@ public class DBRefUtils
   public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
           String source)
   {
-    List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> matches = new ArrayList<>();
     if (dbRefs != null && source != null)
     {
       for (DBRefEntry dbref : dbRefs)
@@ -644,7 +646,7 @@ public class DBRefUtils
       // nothing to do
       return;
     }
-    List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> selfs = new ArrayList<>();
     {
       DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
               sequence.getDBRefs());
@@ -664,11 +666,11 @@ public class DBRefUtils
         selfs.remove(p);
       }
     }
-    List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> toPromote = new ArrayList<>();
 
     for (DBRefEntry p : pr)
     {
-      List<String> promType = new ArrayList<String>();
+      List<String> promType = new ArrayList<>();
       if (sequence.isProtein())
       {
         switch (getCanonicalName(p.getSource()))
-- 
1.7.10.2